edu.duke.cs.osprey/edu.duke.cs.osprey.gui.io/ConfLib

ConfLib

class ConfLib(id: String, name: String, fragments: Map<String, ConfLib.Fragment>, description: String?, citation: String?)

Conformation Library

Constructors

fun ConfLib(id: String, name: String, fragments: Map<String, ConfLib.Fragment>, description: String? = null, citation: String? = null)

Types

sealed class Anchor

AnchorAtomPointer

data class AnchorAtomPointer(anchor: ConfLib.Anchor, index: Int) : ConfLib.AtomPointer

sealed class AnchorCoords

data class AtomInfo(id: Int, name: String, element: Element) : ConfLib.AtomPointer

interface AtomPointer

data class Bond(a: ConfLib.AtomInfo, b: ConfLib.AtomInfo)

object Companion

data class Conf(id: String, name: String, description: String?, coords: Map<ConfLib.AtomInfo, Vector3d>, anchorCoords: Map<ConfLib.Anchor, ConfLib.AnchorCoords>)

ContinuousMotion

sealed class ContinuousMotion

data class Fragment(id: String, name: String, type: String, atoms: List<ConfLib.AtomInfo>, bonds: List<ConfLib.Bond>, anchors: List<ConfLib.Anchor>, confs: Map<String, ConfLib.Conf>, motions: List<ConfLib.ContinuousMotion>)

Functions

fun confRuntimeId(frag: ConfLib.Fragment, conf: ConfLib.Conf): String

A globally unique id for each conformation, assigned at runtime. This id is not intrinsic to the library itself, so should not be persisted anywhere.

fun fragRuntimeId(frag: ConfLib.Fragment): String

A globally unique id for each fragment, assigned at runtime. This id is not intrinsic to the library itself, so should not be persisted anywhere.

getFragmentOrThrow

fun getFragmentOrThrow(fragId: String): ConfLib.Fragment

open override fun toString(): String

Properties

val citation: String? = null

val description: String? = null

val fragments: Map<String, ConfLib.Fragment>

should be a valid TOML key

val name: String

any human-readable short name

val runtimeId: String

A globally unique id for each library, assigned at runtime. This id is not intrinsic to the library itself, so should not be persisted anywhere. Its only purpose is to allow assigning globally unique ids to fragments, conformations, etc at runtime.

Extensions

fun ConfLib.toToml(table: String? = null): String